De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
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De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions. / Li, Ming; Sun, Congjiao; Xu, Naiyi; Bian, Peipei; Tian, Xiaomeng; Wang, Xihong; Wang, Yuzhe; Jia, Xinzheng; Heller, Rasmus; Wang, Mingshan; Wang, Fei; Dai, Xuelei; Luo, Rongsong; Guo, Yingwei; Wang, Xiangnan; Yang, Peng; Hu, Dexiang; Liu, Zhenyu; Fu, Weiwei; Zhang, Shunjin; Li, Xiaochang; Wen, Chaoliang; Lan, Fangren; Siddiki, Amam Zonaed; Suwannapoom, Chatmongkon; Zhao, Xin; Nie, Qinghua; Hu, Xiaoxiang; Jiang, Yu; Yang, Ning.
In: Molecular Biology and Evolution, Vol. 39, No. 4, msac066, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
AU - Li, Ming
AU - Sun, Congjiao
AU - Xu, Naiyi
AU - Bian, Peipei
AU - Tian, Xiaomeng
AU - Wang, Xihong
AU - Wang, Yuzhe
AU - Jia, Xinzheng
AU - Heller, Rasmus
AU - Wang, Mingshan
AU - Wang, Fei
AU - Dai, Xuelei
AU - Luo, Rongsong
AU - Guo, Yingwei
AU - Wang, Xiangnan
AU - Yang, Peng
AU - Hu, Dexiang
AU - Liu, Zhenyu
AU - Fu, Weiwei
AU - Zhang, Shunjin
AU - Li, Xiaochang
AU - Wen, Chaoliang
AU - Lan, Fangren
AU - Siddiki, Amam Zonaed
AU - Suwannapoom, Chatmongkon
AU - Zhao, Xin
AU - Nie, Qinghua
AU - Hu, Xiaoxiang
AU - Jiang, Yu
AU - Yang, Ning
N1 - Publisher Copyright: © 2022 The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
PY - 2022
Y1 - 2022
N2 - The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.
AB - The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is, therefore, necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal subtelomeric regions and microchromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had 3-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute toward the understanding of avian evolution and the improvement of poultry breeding.
KW - avian evolution
KW - chicken
KW - missing genes
KW - noncanonical DNA secondary structure
KW - pan-genome
U2 - 10.1093/molbev/msac066
DO - 10.1093/molbev/msac066
M3 - Journal article
C2 - 35325213
AN - SCOPUS:85128801736
VL - 39
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
SN - 0737-4038
IS - 4
M1 - msac066
ER -
ID: 308898002